Mercurial > repos > sanbi-uwc > build_ctb_gene
changeset 11:517691812452 draft
planemo upload for repository https://github.com/SANBI-SA/tools-sanbi-uwc.git commit 3f5361a7226127ec8b8d6cb5591b5bb4f52bb6fe
| author | sanbi-uwc |
|---|---|
| date | Tue, 17 May 2016 03:45:58 -0400 |
| parents | cb322069c7bc |
| children | 7d49ea27d9f6 |
| files | build_ctb_gene.py build_ctb_gene.xml |
| diffstat | 2 files changed, 15 insertions(+), 29 deletions(-) [+] |
line wrap: on
line diff
--- a/build_ctb_gene.py Mon May 16 10:34:46 2016 -0400 +++ b/build_ctb_gene.py Tue May 17 03:45:58 2016 -0400 @@ -21,43 +21,25 @@ ''' # Check whether the options are specified and saves them into the object - assert args != None + #assert args != None self.args = args def build_ctb_gene(self, output_file1, output_dir, input_file, mount_point): - # cmdline_str = "build_ctb_gene goterms ${}".format(input_file) + #cmdline_str = "build_ctb_gene goterms ${}".format(input_file) + #cmdline_str = "build_ctb_gene goterms --help" cmdline_str = "touch /tmp/foo.bar" build_ctb = False cmdline_str = self.newSplit(cmdline_str) try: check_call(cmdline_str) - build_ctb = True + #build_ctb = True except CalledProcessError: print("Error running the build_ctb_gene gotermS", file=sys.stderr) - # Read the files at the mount point and load the html file - if build_ctb: - files = glob.glob(mount_point) - output_file1 = """<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> - <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> - <head> <meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> - <meta name="generator" content="Galaxy %s tool output - see http://g2.trac.bx.psu.edu/" /> - <title></title> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="toolFormBody"> - <table> - <th>Files</th> - """ - for f in files: - output_file1 += "<tr><td>" + f + "</td></tr>" - output_file1 += """</table></div></body></html>\n""" + self.copy_output_file_to_dataset() + self.args.output_file1 = self.args.outputdir - self.copy_output_file_to_dataset() - return output_file1 - - def newSplit(value): + def newSplit(self, value): lex = shlex.shlex(value) lex.quotes = '"' lex.whitespace_split = True @@ -71,9 +53,12 @@ # retrieve neo4j files to the working gx directory result_file = glob.glob(self.args.mount_point + '/*') - with open(result_file[0], 'rb') as fsrc: - with open(self.args.outputdir, 'wb') as fdest: - shutil.copyfileobj(fsrc, fdest) + for file_name in result_file: + shutil.copy(file_name, self.args.outputdir) + + #with open(result_file[0], 'rb') as fsrc: + #with open(self.args.outputdir, 'wb') as fdest: + #shutil.copy(fsrc, self.args.outputdir) def main(): @@ -103,3 +88,4 @@ if __name__ == "__main__": main() +
--- a/build_ctb_gene.xml Mon May 16 10:34:46 2016 -0400 +++ b/build_ctb_gene.xml Tue May 17 03:45:58 2016 -0400 @@ -9,7 +9,7 @@ <exit_code range="1:" /> </stdio> <command interpreter="python"> - build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2.files_path} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} + build_ctb_gene.py '${outputFile1}' --outputdir ${outputFile2} --input_file ${input_file} --mount_point ${neo4j_data_mount_point} --username ${db_settings.neo4j_db_username} --password ${db_settings.neo4j_db_password} --url ${db_settings.neo4j_db_url} --port ${db_settings.neo4j_db_port} </command> <inputs> <param name="input_file" type="data" format="gff" label="Choose the GFF file" help="Specify the GFF file" optional="False" />